* samtools-0.1.8-11 (r672)

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 896108ac8a1f26bf4c67bb7694fd4f71da4658cd..73624c0a6bdc789d892aa4dc9d89ac07f7adcc38 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -8,7 +8,8 @@ struct __bcf_callaux_t;
 typedef struct __bcf_callaux_t bcf_callaux_t;
 
 typedef struct {
-       int depth;
+       int depth, d[4];
+       int dsum[2], d2sum[2];
        uint64_t sum_Q2;
        float p[25], esum[5];
 } bcf_callret1_t;
@@ -16,7 +17,8 @@ typedef struct {
 typedef struct {
        int a[5]; // alleles: ref, alt, alt2, alt3
        int n, n_alleles, shift, ori_ref, unseen;
-       int depth, rmsQ;
+       int d[4], depth, rmsQ;
+       double davg[2], dstd[2];
        uint8_t *PL;
 } bcf_call_t;
 
@@ -24,7 +26,7 @@ typedef struct {
 extern "C" {
 #endif
 
-       bcf_callaux_t *bcf_call_init(double theta);
+       bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
        void bcf_call_destroy(bcf_callaux_t *bca);
        int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r);
        int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);